gubbins (3.4.3-4) unstable; urgency=medium

  * Team upload.
  * d/control: skip iqtree on i386.

  [ Andreas Tille ]
  * Replace pkg-config with pkgconf in Build-Depends

 -- Michael R. Crusoe <crusoe@debian.org>  Mon, 13 Apr 2026 16:05:27 +0200

gubbins (3.4.3-3) unstable; urgency=medium

  * remove-numba-temporarily.patch: update.
    Cleanup occurrences of numba in python/setup.py.
    Thanks to Adrian Bunk (Closes: #1128512)
  * d/clean: also cleanup leftover csv files. (Closes: #1044465)

 -- Étienne Mollier <emollier@debian.org>  Sat, 21 Feb 2026 09:30:44 +0100

gubbins (3.4.3-2) unstable; urgency=medium

  [ Alexandre Detiste ]
  * New upstream version 3.4.3
  * d/rules: rewrite with shorter syntax, drop old distutils comment
  * Update homepage
  * Drop "Rules-Requires-Root: no"
  * Refresh patches, drop Numpy 2 patch, applied upstream

  [ Étienne Mollier ]
  * d/t/run-example: update the dataset selection.
  * d/watch: convert to v5 Github template.
    Note that sanger-pathogens redirects to nickjcroucher.
  * d/control: drop redundant Priority: optional.
  * d/control: declare compliance to standards version 4.7.3.
  * remove-pkg-resources.patch: new: ditto.
    This patch removes pkg_resouces imports and replaces them by importlib
    where needed.
  * d/control: drop dependency on python3-pkg-resources. (Closes: #1125845)

 -- Étienne Mollier <emollier@debian.org>  Sat, 31 Jan 2026 21:28:16 +0100

gubbins (3.4-2) unstable; urgency=medium

  * d/control: gubbins depends on python3-pkg-resources.
  * numpy2.patch: new: fix further autopkgtest failure with numpy 2.
    (Closes: #1098693)
  * d/control: declare compliance to standards version 4.7.2.

 -- Étienne Mollier <emollier@debian.org>  Fri, 28 Feb 2025 11:09:34 +0100

gubbins (3.4-1) unstable; urgency=medium

  * New upstream version 3.4
  * d/copyright: document missing copyright owners.
    Those are Wellcome Trust Sanger Institute and Imperial College London.
  * d/control: declare compliance to standards version 4.7.0.
  * d/patches/*: normalise last-update timestamp to dep3.

 -- Étienne Mollier <emollier@debian.org>  Sat, 30 Nov 2024 19:00:21 +0100

gubbins (3.3.5-1) unstable; urgency=medium

  * New upstream version 3.3.5
  * iqtree2.patch: unfuzz.
  * python3-shebang.patch: new.
    This fixes a couple of occurrences of unversioned Python interpreter
    declared in the shebang of a couple of scripts.
  * d/control: move to pkgconf.
  * remove-numba-temporarily.patch: new.
    Remove temporarily numba-accelerated pyjar.py functions decorators.
    This allows decorellation of gubbins from numba until the latter is
    available again in trixie.  The change may affect performances, but
    should not affect gubbins results and functionalities otherwise.
  * d/control: promote and comment out dependency on python3-numba.
    This prepares the field for when it will be possible to bring numba
    support back to gubbins, once numba 0.59 or later makes it to trixie.
  * d/t/control: autopkgtests do not depend on python3-numba anymore.
    (Closes: #1058474)

 -- Étienne Mollier <emollier@debian.org>  Wed, 22 May 2024 22:19:47 +0200

gubbins (3.3.3-1) unstable; urgency=medium

  * New upstream version
  * iqtree2.patch: unfuzz.
  * autoupdate_configure.ac.patch: forwarding not needed.

 -- Étienne Mollier <emollier@debian.org>  Sun, 04 Feb 2024 17:45:59 +0100

gubbins (3.3.1-1) unstable; urgency=medium

  [ Andreas Tille ]
  * New upstream version
  * Build-Depends: s/dh-python/dh-sequence-python3/ (routine-update)

  [ Étienne Mollier ]
  * autoupdate_configure.ac.patch: refresh.
  * d/t/run-example: define HOME directory.
    This fixes numba caching issues with the newer test items.
  * d/control: suggest r-core-base.
    This is because gubbins ships a couple of R scripts, although they are
    not critical to proper gubbins operation.
  * gubbins_3.1.0_exe_in_usr_lib.patch: delete leftover.

 -- Étienne Mollier <emollier@debian.org>  Sat, 16 Dec 2023 15:22:50 +0100

gubbins (3.3.0-3) unstable; urgency=medium

  * gubbins_drawer was removed upstream so do not link to it any more
    Closes: #986238
  * Enable building twice in a row
    Closes: #1044465
  * Set upstream metadata fields: Repository.
  * Fix lintian-overrides

 -- Andreas Tille <tille@debian.org>  Thu, 17 Aug 2023 09:25:33 +0200

gubbins (3.3.0-2) unstable; urgency=medium

  * Test-Depends: iqtree

 -- Andreas Tille <tille@debian.org>  Thu, 13 Jul 2023 09:44:07 +0200

gubbins (3.3.0-1) unstable; urgency=medium

  * New upstream version
  * Standards-Version: 4.6.2 (routine-update)
  * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository-Browse.
  * Build-Depends: autoconf-archive
  * autoupdate to avoid warnings from configure.ac
  * Build-Depends: tox and do not override dh_auto_test
  * Test-Depends / Recommends: python3-numba

 -- Andreas Tille <tille@debian.org>  Wed, 12 Jul 2023 21:30:57 +0200

gubbins (2.4.1-5) unstable; urgency=medium

  * Team Upload.
  [ Andreas Tille ]
  * New upstream version
  * Standards-Version: 4.6.0 (routine-update)
  * Build-Depends: python3-scipy <!nocheck>, python3-multiprocess <!nocheck>,
    python3-wheel <!nocheck>
  * Remove trailing whitespace in debian/changelog (routine-update)
  * Adapt test to iqtree2
    Closes: #1005476

  [ Étienne Mollier ]
  * d/control: update uploader address
  * d/watch: bump to uscan version 4 and fix broken link to github

  [ Nilesh Patra ]
  * Switch from nosetest -> pytest

 -- Andreas Tille <tille@debian.org>  Sun, 13 Feb 2022 15:17:59 +0100

gubbins (2.4.1-4) unstable; urgency=medium

  * Team upload.
  * Fix symlink to right place (Closes: #986238)

 -- Nilesh Patra <nilesh@debian.org>  Sun, 04 Apr 2021 16:11:03 +0530

gubbins (2.4.1-3) unstable; urgency=medium

  [ Andreas Tille ]
  * Remove non-working e-mail addresses
  * Remove Aidan Delaney from Uploaders since his e-mail is bouncing

  [ Étienne Mollier ]
  * Added src/ to PATH for build time tests.  (Closes: #971111)
  * Fixed spelling error in gubbins binaries.
  * Added myself to Uploaders.
  * debhelper-compat 13 (routine-update)

 -- Étienne Mollier <etienne.mollier@mailoo.org>  Mon, 02 Nov 2020 13:22:13 +0100

gubbins (2.4.1-2) unstable; urgency=medium

  * Versioned Build-Depends: raxml (>= 8.2.12+dfsg-5)
    Closes: #955006
  * Add salsa-ci file (routine-update)
  * Rules-Requires-Root: no (routine-update)

 -- Andreas Tille <tille@debian.org>  Thu, 02 Apr 2020 17:03:51 +0200

gubbins (2.4.1-1) unstable; urgency=medium

  * Team upload.
  * New upstream version
  * Standards-Version: 4.5.0
  * Remove trailing whitespace in debian/changelog (routine-update)
  * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository.
  * Specified raxml version from Dockerfile - test complained on i386

 -- Steffen Moeller <moeller@debian.org>  Wed, 22 Jan 2020 12:30:58 +0100

gubbins (2.4.0-2) unstable; urgency=medium

  * Team upload.
  * Fix run_gubbins wrapper (Sascha Steinbiss)
  * raxml needed as default method at runtime - turned back into
    hard dependency (suggested by Sascha)

 -- Steffen Moeller <moeller@debian.org>  Thu, 09 Jan 2020 02:31:16 +0100

gubbins (2.4.0-1) unstable; urgency=medium

  * Team upload.
  * New upstream version

  * Removing debian/patches/disable_test.patch which apparently upstream
    addressed in its new release.
  * Added build-time (testing) and recommended runtime dependency on iqtree
  * Demoted runtime-dependencies to fasttree and raxml to recommended

 -- Steffen Moeller <moeller@debian.org>  Wed, 08 Jan 2020 12:59:28 +0100

gubbins (2.3.5-1) unstable; urgency=medium

  * Team upload.
  * New upstream version
  * debhelper-compat 12
  * Standards-Version: 4.4.1
  * Secure URI in copyright format
  * Set upstream metadata fields: Repository, Repository-Browse.
  * Cleaner clean
  * Reported autogenerated files in source tree to upstream

 -- Steffen Moeller <moeller@debian.org>  Sat, 21 Dec 2019 00:00:10 +0100

gubbins (2.3.4-1) unstable; urgency=medium

  * New upstream version
  * debhelper 11
  * Point Vcs fields to salsa.debian.org
  * Standards-Version: 4.2.1
  * debian/rules:
     - Respect DEB_BUILD_OPTIONS in override_dh_auto_test
     - Do not parse d/changelog
  * Remove unneeded Testsuite: autopkgtest

 -- Andreas Tille <tille@debian.org>  Wed, 26 Sep 2018 16:48:49 +0200

gubbins (2.3.1-1) unstable; urgency=medium

  * Team upload.
  * New upstream release.
  * Bump Standards-Version.

 -- Sascha Steinbiss <satta@debian.org>  Sun, 01 Oct 2017 11:59:00 +0100

gubbins (2.2.0-1) unstable; urgency=medium

  * Team upload.
  * New upstream release.

 -- Sascha Steinbiss <satta@debian.org>  Thu, 03 Nov 2016 15:25:15 +0100

gubbins (2.1.0-2) unstable; urgency=medium

  * Team upload.
  * Disable tests to address FTBFS caused by failed build time tests
    relying on external dependencies.
    Closes: #839320

 -- Sascha Steinbiss <satta@debian.org>  Wed, 26 Oct 2016 14:26:18 +0200

gubbins (2.1.0-1) unstable; urgency=medium

  * New upstream release

 -- Andreas Tille <tille@debian.org>  Fri, 09 Sep 2016 10:02:51 +0200

gubbins (2.0.0-1) unstable; urgency=medium

  * Team upload.
  * New upstream release.
  * Fix Vcs-Git.
  * Remove dependencies on FastML.
  * Update manpage dates.
  * Bump Standards-Version.
  * Add autopkgtests.

 -- Sascha Steinbiss <satta@debian.org>  Wed, 20 Jul 2016 13:08:22 +0000

gubbins (1.4.9-1) unstable; urgency=medium

  * New upstream version
  * Build-Depends: fastml

 -- Andreas Tille <tille@debian.org>  Wed, 20 Apr 2016 19:55:22 +0200

gubbins (1.4.7-1) unstable; urgency=medium

  * New upstream version
  * cme fix dpkg-control
  * enhance hardening

 -- Andreas Tille <tille@debian.org>  Sat, 19 Mar 2016 22:10:44 +0100

gubbins (1.4.5-1) unstable; urgency=medium

  * New upstream version
  * Secure Vcs-Git

 -- Andreas Tille <tille@debian.org>  Wed, 27 Jan 2016 19:53:33 +0100

gubbins (1.4.4-2) unstable; urgency=medium

  * do not build-dep on python3-all-dev
    Closes: #809489

 -- Andreas Tille <tille@debian.org>  Thu, 31 Dec 2015 12:49:12 +0100

gubbins (1.4.4-1) unstable; urgency=medium

  * New upstream version
    Closes: #807150

 -- Andreas Tille <tille@debian.org>  Wed, 09 Dec 2015 17:07:44 +0100

gubbins (1.4.3-1) unstable; urgency=medium

  * Initial Debian release (Closes: #764232, #806726)

 -- Andreas Tille <tille@debian.org>  Mon, 30 Nov 2015 15:10:52 +0100
